diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/search.py | 171 |
1 files changed, 47 insertions, 124 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py index 8ce51e3..d25f362 100644 --- a/gn3/api/search.py +++ b/gn3/api/search.py @@ -40,28 +40,6 @@ def combine_queries(operator: int, *queries: xapian.Query) -> xapian.Query: return reduce(partial(xapian.Query, operator), queries) -def query_subqueries(query: xapian.Query) -> list[xapian.Query]: - """Return list of child queries in query.""" - return [query.get_subquery(i) for i in range(query.get_num_subqueries())] - - -def query_terms(query: xapian.Query) -> list[str]: - """Return list of terms in query.""" - # Unfortunately, the TermIterator from python xapian bindings seems - # buggy. So, we resort to traversing the query tree. - # python xapian bindings do not expose xapian.Query.LEAF_TERM. This is - # most likely a bug. - leaf_type = 100 - if query.get_type() == leaf_type: - # We have no choice but to access the protected _get_terms_begin method. - # pylint: disable=protected-access - return [query._get_terms_begin().get_term().decode("utf-8")] - else: - return reduce(lambda result, subquery: result + query_terms(subquery), - query_subqueries(query), - []) - - class FieldProcessor(xapian.FieldProcessor): """ Field processor for use in a xapian query parser. @@ -200,110 +178,55 @@ def parse_location_field(species_query: xapian.Query, .maybe(xapian.Query.MatchNothing, make_query)) -def parse_synteny_field(synteny_prefix: str, query: bytes) -> xapian.Query: - """Parse synteny field and return a xapian query.""" - if query.decode("utf-8") in ["on", "off"]: - return xapian.Query(synteny_prefix + query.decode("utf-8")) - else: - return xapian.Query(xapian.Query.OP_INVALID) - - -def is_synteny_on(synteny_prefix: str, query: xapian.Query) -> bool: - """Check if synteny search is requested in query.""" - return synteny_prefix + "on" in query_terms(query) - - -def remove_synteny_field(synteny_prefix: str, query: xapian.Query, - parent_operator: int = xapian.Query.OP_AND) -> xapian.Query: - """Return a new query with the synteny field removed.""" - # Note that this function only supports queries that exclusively use the - # AND, OR, FILTER, WEIGHT, RANGE and INVALID operators. - # python xapian bindings do not expose xapian.Query.LEAF_TERM. This is - # most likely a bug. - leaf_type = 100 - # Handle leaf node. - if query.get_type() == leaf_type: - if not any(term.startswith(synteny_prefix) for term in query_terms(query)): - return query - elif parent_operator in [xapian.Query.OP_AND, xapian.Query.OP_FILTER]: - return xapian.Query.MatchAll - elif parent_operator == xapian.Query.OP_OR: - return xapian.Query.MatchNothing - else: - raise ValueError("Unexpected operator in query", query.get_type()) - # Recurse on non-leaf nodes with the AND, OR or FILTER operators as root. - elif query.get_type() in (xapian.Query.OP_AND, xapian.Query.OP_OR, - xapian.Query.OP_FILTER, xapian.Query.OP_SCALE_WEIGHT): - return combine_queries(query.get_type(), - *[remove_synteny_field(synteny_prefix, subquery, query.get_type()) - for subquery in query_subqueries(query)]) - # Return other supported non-leaf nodes verbatim. - elif query.get_type() in [xapian.Query.OP_VALUE_RANGE, xapian.Query.OP_INVALID]: - return query - # Raise an exception on unsupported non-leaf nodes. - else: - raise ValueError("Unexpected operator in query", query.get_type()) - - def parse_query(synteny_files_directory: Path, query: str): """Parse search query using GeneNetwork specific field processors.""" - synteny_prefix = "XSYN" - - def make_query_parser(synteny: bool) -> xapian.QueryParser: - queryparser = xapian.QueryParser() - queryparser.set_stemmer(xapian.Stem("en")) - queryparser.set_stemming_strategy(queryparser.STEM_SOME) - species_prefix = "XS" - chromosome_prefix = "XC" - queryparser.add_boolean_prefix("author", "A") - queryparser.add_boolean_prefix("species", species_prefix) - queryparser.add_boolean_prefix("group", "XG") - queryparser.add_boolean_prefix("tissue", "XI") - queryparser.add_boolean_prefix("dataset", "XDS") - queryparser.add_boolean_prefix("symbol", "XY") - queryparser.add_boolean_prefix("chr", chromosome_prefix) - queryparser.add_boolean_prefix("peakchr", "XPC") - queryparser.add_prefix("description", "XD") - queryparser.add_prefix("synteny", FieldProcessor(partial(parse_synteny_field, - synteny_prefix))) - range_prefixes = ["mean", "peak", "mb", "peakmb", "additive", "year"] - for i, prefix in enumerate(range_prefixes): - queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":")) - - # Add field processors for location shorthands. - species_shorthands = {"Hs": "human", - "Mm": "mouse"} - for shorthand, species in species_shorthands.items(): - field_processors = [partial(parse_location_field, - xapian.Query(species_prefix + species), - chromosome_prefix, - range_prefixes.index("mb"), - Just)] - # If human and synteny is requested, add liftover. - # With synteny search, we search for the same gene sequences - # across different species. But, the same gene sequences may be - # present in very different chromosomal positions in different - # species. So, we first liftover. - if shorthand == "Hs" and synteny: - chain_files = {"mouse": "hg19ToMm10-chains.over.chain.gz"} - for lifted_species, chain_file in chain_files.items(): - field_processors.append( - partial(parse_location_field, - xapian.Query(species_prefix + lifted_species), - chromosome_prefix, - range_prefixes.index("mb"), - partial(liftover_interval, - synteny_files_directory / chain_file))) - queryparser.add_boolean_prefix( - shorthand, - FieldProcessor(field_processor_or(*field_processors))) - return queryparser - - return remove_synteny_field( - synteny_prefix, - make_query_parser(is_synteny_on(synteny_prefix, - make_query_parser(False).parse_query(query))) - .parse_query(query)) + queryparser = xapian.QueryParser() + queryparser.set_stemmer(xapian.Stem("en")) + queryparser.set_stemming_strategy(queryparser.STEM_SOME) + species_prefix = "XS" + chromosome_prefix = "XC" + queryparser.add_boolean_prefix("author", "A") + queryparser.add_boolean_prefix("species", species_prefix) + queryparser.add_boolean_prefix("group", "XG") + queryparser.add_boolean_prefix("tissue", "XI") + queryparser.add_boolean_prefix("dataset", "XDS") + queryparser.add_boolean_prefix("symbol", "XY") + queryparser.add_boolean_prefix("chr", chromosome_prefix) + queryparser.add_boolean_prefix("peakchr", "XPC") + queryparser.add_prefix("description", "XD") + range_prefixes = ["mean", "peak", "mb", "peakmb", "additive", "year"] + for i, prefix in enumerate(range_prefixes): + queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":")) + + # Add field processors for synteny triplets. + species_shorthands = {"Hs": "human", + "Mm": "mouse"} + for shorthand, species in species_shorthands.items(): + field_processors = [partial(parse_location_field, + xapian.Query(species_prefix + species), + chromosome_prefix, + range_prefixes.index("mb"), + Just)] + # With synteny search, we search for the same gene sequences + # across different species. But, the same gene sequences may be + # present in very different chromosomal positions in different + # species. So, we first liftover. + # TODO: Implement liftover and synteny search for species other than + # human. + if shorthand == "Hs": + chain_files = {"mouse": "hg19ToMm10-chains.over.chain.gz"} + for lifted_species, chain_file in chain_files.items(): + field_processors.append( + partial(parse_location_field, + xapian.Query(species_prefix + lifted_species), + chromosome_prefix, + range_prefixes.index("mb"), + partial(liftover_interval, + synteny_files_directory / chain_file))) + queryparser.add_boolean_prefix( + shorthand, + FieldProcessor(field_processor_or(*field_processors))) + return queryparser.parse_query(query) @search.route("/") |